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''In progress''

Name

sxresolution - Local Resolution: Compute local resolution of a map.

Usage

In progress Usage in command lines:

sxlocres.py firstvolume secondvolume maskfile outputfile --wn=window_size --step=shell_step_size --cutoff=res_cutoff --res_overall=overall_resolution --radius=radius --fsc=output_file_name --MPI

Typical usage

sxlocres exists in for both MPI and non-MPI versions.

mpirun -np 32 sxlocres.py refinementdir/main002/vol0.hdf refinementdir/main002/vol2.hdf locres.hdf --cutoff=0.5 --radius=28 --res_overall=0.3 --fsc=fscvol.txt --MPI

Input

firstvolume
First half-volume: (default required string)
secondvolume
Second half-volume: (default required string)
maskfile
3D mask: Defines the region where the local filtering should be applied. (default none)
wn
FSC window size: Defines the size of window where the local real-space FSC is computed. (default 7)
step
Fourier shell step size [Pixels]: (default 1.0)
cutoff
Resolution cut-off [1/Pixel]: Cut-off for the FSC. By default it goes to the Nyquist frequencies. (default 0.5)
radius
Mask radius [Pixels]: In case no mask is provided, a hard sphere of this radius will be used. (default -1)
res_overall
Overall resolution calibration (0 to 0.5). See Description below for details. (default -1)
  • The remaining parameters are optional.
  • MPI
    Use MPI: (default False)

    Output

    outputfile

    Output volume: Each voxel contains the resolution for this area in absolute frequency units. (default required string)

    fsc
    FSC output file: Contains the overall FSC curve computed by rotational averaging of local resolution values. It is truncated to res_overall. (default no curve)

    Description

    • Local resolution values are computed within small windowed areas (size wn^3). Due to small sample size the values are inaccurate and tend to underestimate resolution. Therefore, option res_overall allows to calibrate the average value of all local resolutions to the overall resolution, as estimated by the FSC between two full size volumes. I This value has to be independently obtained by the user - for example using sximgstat.py to compute (masked) FSC from half-volumes and reading the absolute frequency crresponding to 0.5 (or other) cut-off value.

    Method

    Reference

    Author / Maintainer

    Pawel Penczek

    Keywords

    category 1
    APPLICATIONS

    Files

    sxresolution.py

    See also

    Maturity

    stable
    works for most people, has been tested; test cases/examples available.

    Bugs

    None. It is perfect.

    sxresolution (last edited 2020-09-15 14:37:28 by penczek)